Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
5158d4df
Commit
5158d4df
authored
Apr 06, 2015
by
Peter van 't Hof
Browse files
Added start for Shiva report
parent
a83aeb9a
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ShivaVariantcalling.ssp
0 → 100644
View file @
5158d4df
#import(nl.lumc.sasc.biopet.core.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var sampleId: Option[String] = None %>
#{
val fields = List("Hom", "HomVar", "HomRef", "NoCall", "Variant", "NonInformative", "Total")
val samples = sampleId match {
case Some(sample) => List(sample.toString)
case _ => summary.samples.toList
}
}#
<table>
<thead><tr><th>Sample</th>
#for (field <- fields) <th>${field}</th> #end
</tr></thead>
<tbody>
#for (sample <- samples.toList.sorted)
<tr><td>${sample}</td>
#for (field <- fields)
<td>${summary.getSampleValue(sample, "shivavariantcalling", "stats", "multisample-vcfstats-final", "genotype", field)}</td>
#end
</tr>
#end
</tbody>
</table>
\ No newline at end of file
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
0 → 100644
View file @
5158d4df
package
nl.lumc.sasc.biopet.pipelines.shiva
import
nl.lumc.sasc.biopet.core.report.
{
MultisampleReportBuilder
,
ReportPage
}
import
nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
/**
* Created by pjvan_thof on 3/30/15.
*/
object
ShivaReport
extends
MultisampleReportBuilder
{
def
samplePage
(
sampleId
:
String
,
args
:
Map
[
String
,
Any
])
=
{
ReportPage
(
Map
(
"Libraries"
->
generateLibraryPage
(
args
)),
Map
(
"Variantcalling"
->
"/nl/lumc/sasc/biopet/core/report/ShivaVariantcalling.ssp"
),
args
)
}
def
libraryPage
(
libId
:
String
,
args
:
Map
[
String
,
Any
])
=
{
ReportPage
(
Map
(
"Flexiprep"
->
FlexiprepReport
.
indexPage
),
Map
(),
args
)
}
def
reportName
=
"Title Test"
def
generalPage
=
ReportPage
(
Map
(),
Map
(
"Variantcalling"
->
"/nl/lumc/sasc/biopet/core/report/ShivaVariantcalling.ssp"
,
"Flexiprep"
->
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepSummary.ssp"
),
Map
())
// FIXME: Not yet finished
}
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment